As fighting began to recapture Fallujah from militants of the self-declared Islamic State (IS), Iraq’s most influential Shiite cleric went to unusual lengths to warn against sectarian killing.

“Don’t be extreme … don’t be treacherous,” said Grand Ayatollah Ali Sistani, who commands a massive following and effectively recruited tens of thousands of the Shiite militiamen that have been fighting IS. “Don’t kill an old man, nor a boy, nor a woman.... Don’t cut a tree unless you have to.”

Mr. Sistani’s call to respect the “ethics of jihad,” by invoking the words of the Muslim Prophet Mohammad, signals his desire both to calm Iraq’s sectarian fires and to lessen anti-Shiite propaganda.

Already many influential Sunnis in the region, including the ultra-conservative IS, are casting the Fallujah showdown as another episode of ethnic cleansing by Iraq’s unruly Shiite militias and the Shiite-dominated Iraqi Army.

The stakes are high in a Sunni city where the UN and aid agencies say 50,000 civilians have been trapped. IS is reportedly preventing them from leaving, at the end of months of siege that have caused food and medicine shortages – or even forcing them to join the fight.

Iraqi armed forces, backed by a coalition of Shiite militias known as Hashid Shaabi (Popular Mobilization Forces), have stepped up shelling of Fallujah in the past week. The Army has yet to enter the city limits or even fully encircle the city. The militias are not expected to participate in the main assault, to avoid inflaming sectarian tensions.

But fears have grown among Sunnis in the city – fanned by social media and commentary – that the Shiite militias could repeat past atrocities and engage in revenge killings.

“[Sistani] as much as anyone realizes that if Iraq is ever to get back to that notion of equal citizenship and a civic state, the way [IS] is driven out of these territories is going to be absolutely crucial,” says Toby Dodge, author of the book "Iraq: From War to a New Authoritarianism."

“In the Hashid Shaabi, he has created a monster he doesn’t control, which doesn’t back his ultimate aim, and he’s seeking through very powerful messaging to restrain them as much as possible.”

Sistani’s intervention resonates even more – and indicates the serious danger the reclusive, octogenarian cleric sees of the Fallujah fight exacerbating sectarian conflict – considering that he gave up delivering Friday sermons a month ago, adds Mr. Dodge, who is director of the Middle East Center at the London School of Economics.

Sistani's 2014 fatwa that resurrected Shiite militias

In 2014, Sistani issued an unprecedented fatwa, which described it a duty of all able-bodied men to take up arms in defense. It came as IS crossed from Syria to seize control of Iraq’s second city of Mosul, then swept south as the Iraqi Army collapsed, vowing to capture Baghdad and destroy “apostate” Shiite shrines in Karbala and Najaf.

Tens of thousands of mostly Shiite men obeyed that call, and since then, Iraq’s militias – backed by Iran – have been instrumental in reversing the IS advance, even in predominantly Sunni areas like Anbar province, where Fallujah is located.

But the price has been high, with human rights groups documenting brutal anti-Sunni actions and even ethnic cleansing by those Shiite militias, which has stoked Iraq’s sectarian tensions.

As IS has been pushed back, more than a few of Iraq’s Sunni minority – beneficiaries for decades during the rule of Sunni autocrat Saddam Hussein, but disenfranchised by the American invasion of 2003 – have said they feel more threatened by Shiite forces than by the Sunni IS presence, violent as that has been.

The Association of Muslim Scholars of Iraq, a hard-line group that for more than a decade has presented itself as a voice of Sunnis, called the Fallujah advance “an unjust aggression, a reflection of the vengeful spirit that the forces of evil harbor against this city.”

And Human Rights Watch this week called for accountability mechanisms for Iraqi militias to protect civilians and “to ensure that new abuses do not breed resentment feeding a resurgence of IS-like groups.”

Few Sunnis forget the role that Shiite militias first played in Iraq, especially in 2006 and 2007, when ethnic cleansing of Baghdad neighborhoods and other killings – often at the hands of Shiite groups – resulted in death tolls as high as 3,000 per month in the capital alone.

Sistani no doubt recognizes the extent to which IS could exploit new abuses to fuel its own narrative – and credibility.

“The government’s blessing of the involvement of Shia militias in the fight against IS has further confirmed its bias in the eyes of Sunnis,” wrote Lina Khatib, head of the Middle East and North Africa program at the Chatham House think tank in London, in an analysis for CNN.

“For those Sunnis in Fallujah who back IS, the involvement of Shia militias will drive them even closer to IS,” says Ms. Khatib. “While for those … who do not support IS, being liberated from it at the hands of Shia militias is a case of removing one tyrant to be replaced by another.”

Tikrit battle signaled lessons learned

Iraqi Prime Minister Haider al-Abadi, a Shiite, has vowed to reverse the openly Shiite-first policies of his predecessor Nuri al-Maliki, whose exclusionary tactics and clumsy use of predominantly Shiite forces in Sunni areas for years alienated many before 2014. That prompted many Sunni tribes to rise up against the Baghdad leadership and welcome IS as saviors at first.

Mr. Abadi’s ability to transform Iraq’s sectarianism may be limited. But the recapture of Tikrit from IS in spring 2015, with its swift departure of Shiite militia forces and quick rebuilding efforts, appeared to reflect lessons learned.

“There has undoubtedly been sectarian cleansing, murders, revenge attacks…. Clearly the Hashid have been guilty of sectarian war crimes,” says Dodge. “Haider al-Abadi got on top of that with Tikrit…. Their role was minimized, and I assume that that role will be minimal or greatly restricted in Fallujah.”

Indeed, Hadi al-Amiri, the leader of one of the largest militias in the Shiite coalition, has said militias will not enter Fallujah unless the Iraqi Army fails to dislodge IS.

'PM is aware of the ramifications'

Expelling Sunni extremists has been part of Fallujah’s history since 2004, when the US military cleared the city of Al Qaeda in fierce door-to-door combat, which left the city in ruins. Back then, US officers noted that the city, just west of Baghdad, had become an insurgent center for making suicide car bombs to strike the capital, and for kidnapping and extortion.

For the Iraqi forces today, Fallujah plays a similar role of threatening Baghdad, which in recent weeks has been struck by a spate of suicide car bombs, killing more than 200. This bid to recapture Fallujah is the latest in a chain of advances against IS in Iraq and Syria, which has seen the jihadists lose control of significant swaths of territory in the past year – including in December the provincial capital of Ramadi, which was largely wrecked in the process.

Iraqi officers reported an IS counter-attack on Tuesday morning that resulted in casualties on both sides. But what may shape the aftermath of the fight is the manner in which IS is eventually forced out – and whether an aging cleric’s plea for restraint is heard on the Iraqi battlefield.

“There are huge dangers in using an informal militia­ to do any of the work in Fallujah. But those dangers are recognized,” says Dodge. “The PM at least is aware of the ramifications that widespread sectarian bloodletting would have.”

Follow Scott Peterson on Twitter at @peterson__scott

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